

The maximum flux transition path (MFTP) 

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@string{JSP = "J.\ Stat.\ Phys."}
@string{PRL = "Phys.\ Rev.\ Lett."}
@string{PNAS = "Proc.\ Natl.\ Acad.\ Sci.\ USA"}
@string{JCP = "J.\ Chem.\ Phys."}
@string{JPCB = "J.\ Phys.\ Chem.\ B"}
@string{PSFB  = "PROTEINS:\ Struc.,\ Func.,\ and Bioinformatics"}

@article{Ortoleva:2008p1554,
author = {P Ortoleva}, 
journal = JSP,
title = {Curvilinear all-atom multiscale ({CAM}) theory of macromolecular dynamics},
abstract = {Abstract A method is introduced for simulating long timescale macromolecular structural fluctuations and transitions with atomic-scale detail. The N-atom Liouville equation for the macromolecule/host medium system provides the starting point for the analysis. Order pa- ...},
year = {2008},
month = {Jan},
date-added = {2011-08-30 10:46:36 -0400},
date-modified = {2011-08-30 10:46:36 -0400},
pmid = {10413776166837491907related:wxjHyj8qhZAJ},
URL = {http://www.springerlink.com/index/L1447085035G6344.pdf},
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@article{Altis:2007p1500,
author = {A Altis and P Nguyen and G Stock}, 
journal = PRL,
title = {How complex is the dynamics of peptide folding?},
abstract = {Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with ...},
year = {2007},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {15872772487195554585related:GXPiw3pqR9wJ},
URL = {http://link.aps.org/doi/10.1103/PhysRevLett.98.028102},
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@article{Nguyen:2007p1501,
author = {P Nguyen and R Hegger and G Stock}, 
journal = JCP,
title = {Dihedral angle principal component analysis of molecular dynamics simulations},
abstract = {It has recently been suggested by Mu et al. [Proteins [bold 58], 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates ...},
year = {2007},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {1022371532299617480related:yMQw630xMA4J},
URL = {http://link.aip.org/link/?JCPSA6/126/244111/1},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p1501},
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@article{Nguyen:2008p1502,
author = {P Nguyen and R Hegger and G Stock}, 
journal = JCP,
title = {Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis},
abstract = {A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis (dPCA), which avoids artifacts due to the ...},
year = {2008},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {15920830421529783725related:re2DjOom8twJ},
URL = {http://link.aip.org/link/?JCPSA6/128/245102/1},
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@article{Hu:2008p1447,
author = {J Hu and A Ma{\ldots}}, 
journal = PNAS,
title = {A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT},
abstract = {... Ma A ,; Dinner AR. (2005) Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 109:6769--6779. Medline. ↵.},
year = {2008},
month = {Jan},
date-added = {2011-08-29 20:46:20 -0400},
date-modified = {2011-08-29 20:46:20 -0400},
pmid = {2408966963801925689related:OagQubBebiEJ},
URL = {http://www.pnas.org/content/105/12/4615.short},
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@article{Qi:2010p1445,
author = {B Qi and S Muff and A Caflisch and A.R Dinner}, 
journal = {The Journal of Physical Chemistry B},
title = {Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a β-Sheet Miniprotein},
number = {20},
pages = {6979--6989},
volume = {114},
year = {2010},
date-added = {2011-08-29 20:37:05 -0400},
date-modified = {2011-08-29 20:38:22 -0400},
pmid = {10068942009870876633related:2X9cEmkRvIsJ},
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@article{Ma:2005p1444,
author = {A Ma and R Aaron}, 
journal = {The Journal of Physical Chemistry B},
title = {Automatic method for identifying reaction coordinates in complex systems},
number = {14},
pages = {6769--6779},
volume = {109},
year = {2005},
date-added = {2011-08-29 10:29:40 -0400},
date-modified = {2011-08-29 10:32:51 -0400},
pmid = {5495015443088609266related:8g-VgG43QkwJ},
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@article{Zhao:2009p1443,
author = {R Zhao and J Shen and R.D Skeel}, 
journal = {Journal of chemical theory and computation},
title = {Maximum flux transition paths of conformational change},
year = {2009},
date-added = {2011-08-29 10:02:48 -0400},
date-modified = {2011-08-29 10:03:51 -0400},
pmid = {9118122886363458929related:ca0NjHQUin4J},
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@article{Peng:2010p1442,
author = {Cheng Peng and Liqing Zhang and Teresa Head-Gordon}, 
journal = {Biophysj},
title = {Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions},
number = {10},
pages = {2356--2364},
volume = {98},
year = {2010},
month = {May},
date-added = {2011-08-29 09:37:19 -0400},
date-modified = {2011-08-29 09:37:19 -0400},
doi = {10.1016/j.bpj.2010.01.044},
URL = {http://dx.doi.org/10.1016/j.bpj.2010.01.044},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2010/Peng/Peng_2010_Biophysj.pdf},
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@article{RaAr09,
author = {A Ramanathan and P.K Agarwal}, 
journal = JPCB,
title = {Computational identification of slow conformational fluctuations in proteins},
number = {52},
pages = {16669--16680},
volume = {113},
year = {2009},
date-added = {2011-06-28 01:37:34 -0400},
date-modified = {2011-06-28 01:38:31 -0400},
pmid = {14938217343728256272related:EIWALoc1T88J},
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@article{Schuyler:2009p562,
author = {Adam D Schuyler and Robert L Jernigan and Pradman K Qasba and Boopathy Ramakrishnan and Gregory S Chirikjian}, 
journal = PSFB,
title = {Iterative cluster-NMA: A tool for generating conformational transitions in proteins},
number = {3},
pages = {760--776},
volume = {74},
year = {2009},
month = {Feb},
date-added = {2011-06-28 01:39:20 -0400},
date-modified = {2011-06-28 01:39:20 -0400},
doi = {10.1002/prot.22200},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2009/Schuyler/Schuyler_2009_Proteins%20Structure%20Function%20and%20Bioinformatics.pdf},
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@article{Skjaerven:2010p558,
author = {Lars Skjaerven and Aurora Martinez and Nathalie Reuter}, 
journal = PSFB,
title = {Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit},
number = {1},
pages = {232--243},
volume = {79},
year = {2010},
month = {Nov},
date-added = {2011-06-28 01:36:34 -0400},
date-modified = {2011-06-28 01:36:34 -0400},
doi = {10.1002/prot.22875},
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@article{Singharoy:2011p1441,
author = {A Singharoy and S Cheluvaraja and P Ortoleva}, 
journal = JCP,
title = {Order parameters for macromolecules: Application to multiscale simulation},
abstract = {},
number = {4},
pages = {044104},
volume = {134},
year = {2011},
month = {Jan},
keywords = {}, 
date-added = {2011-08-28 21:27:12 -0400},
date-modified = {2011-08-28 21:27:12 -0400},
doi = {10.1063/1.35234532.2},
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